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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 9-91724406-G-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=9&pos=91724406&ref=G&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "9",
"pos": 91724406,
"ref": "G",
"alt": "A",
"effect": "synonymous_variant",
"transcript": "ENST00000375708.4",
"consequences": [
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.2088C>T",
"hgvs_p": "p.Tyr696Tyr",
"transcript": "NM_004560.4",
"protein_id": "NP_004551.2",
"transcript_support_level": null,
"aa_start": 696,
"aa_end": null,
"aa_length": 943,
"cds_start": 2088,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 2353,
"cdna_end": null,
"cdna_length": 4158,
"mane_select": "ENST00000375708.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.2088C>T",
"hgvs_p": "p.Tyr696Tyr",
"transcript": "ENST00000375708.4",
"protein_id": "ENSP00000364860.3",
"transcript_support_level": 1,
"aa_start": 696,
"aa_end": null,
"aa_length": 943,
"cds_start": 2088,
"cds_end": null,
"cds_length": 2832,
"cdna_start": 2353,
"cdna_end": null,
"cdna_length": 4158,
"mane_select": "NM_004560.4",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 13,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1668C>T",
"hgvs_p": "p.Tyr556Tyr",
"transcript": "ENST00000375715.5",
"protein_id": "ENSP00000364867.1",
"transcript_support_level": 1,
"aa_start": 556,
"aa_end": null,
"aa_length": 704,
"cds_start": 1668,
"cds_end": null,
"cds_length": 2115,
"cdna_start": 2265,
"cdna_end": null,
"cdna_length": 2993,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.2079C>T",
"hgvs_p": "p.Tyr693Tyr",
"transcript": "XM_017014762.2",
"protein_id": "XP_016870251.1",
"transcript_support_level": null,
"aa_start": 693,
"aa_end": null,
"aa_length": 940,
"cds_start": 2079,
"cds_end": null,
"cds_length": 2823,
"cdna_start": 9799,
"cdna_end": null,
"cdna_length": 11604,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1668C>T",
"hgvs_p": "p.Tyr556Tyr",
"transcript": "XM_005252008.5",
"protein_id": "XP_005252065.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 803,
"cds_start": 1668,
"cds_end": null,
"cds_length": 2412,
"cdna_start": 2113,
"cdna_end": null,
"cdna_length": 3918,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1668C>T",
"hgvs_p": "p.Tyr556Tyr",
"transcript": "XM_006717121.4",
"protein_id": "XP_006717184.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 803,
"cds_start": 1668,
"cds_end": null,
"cds_length": 2412,
"cdna_start": 2910,
"cdna_end": null,
"cdna_length": 4715,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 9,
"exon_rank_end": null,
"exon_count": 9,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1668C>T",
"hgvs_p": "p.Tyr556Tyr",
"transcript": "XM_047423434.1",
"protein_id": "XP_047279390.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 803,
"cds_start": 1668,
"cds_end": null,
"cds_length": 2412,
"cdna_start": 3208,
"cdna_end": null,
"cdna_length": 5013,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1668C>T",
"hgvs_p": "p.Tyr556Tyr",
"transcript": "XM_047423435.1",
"protein_id": "XP_047279391.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 803,
"cds_start": 1668,
"cds_end": null,
"cds_length": 2412,
"cdna_start": 2342,
"cdna_end": null,
"cdna_length": 4147,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1668C>T",
"hgvs_p": "p.Tyr556Tyr",
"transcript": "XM_047423436.1",
"protein_id": "XP_047279392.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 803,
"cds_start": 1668,
"cds_end": null,
"cds_length": 2412,
"cdna_start": 2239,
"cdna_end": null,
"cdna_length": 4044,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.1668C>T",
"hgvs_p": "p.Tyr556Tyr",
"transcript": "XM_047423437.1",
"protein_id": "XP_047279393.1",
"transcript_support_level": null,
"aa_start": 556,
"aa_end": null,
"aa_length": 803,
"cds_start": 1668,
"cds_end": null,
"cds_length": 2412,
"cdna_start": 2277,
"cdna_end": null,
"cdna_length": 4082,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "Y",
"aa_alt": "Y",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"synonymous_variant"
],
"exon_rank": 3,
"exon_rank_end": null,
"exon_count": 3,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "c.885C>T",
"hgvs_p": "p.Tyr295Tyr",
"transcript": "XM_005252009.4",
"protein_id": "XP_005252066.1",
"transcript_support_level": null,
"aa_start": 295,
"aa_end": null,
"aa_length": 542,
"cds_start": 885,
"cds_end": null,
"cds_length": 1629,
"cdna_start": 993,
"cdna_end": null,
"cdna_length": 2798,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 11,
"exon_rank_end": null,
"exon_count": 11,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"hgvs_c": "n.2556C>T",
"hgvs_p": null,
"transcript": "ENST00000550066.5",
"protein_id": null,
"transcript_support_level": 2,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4360,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
}
],
"gene_symbol": "ROR2",
"gene_hgnc_id": 10257,
"dbsnp": "rs10992063",
"frequency_reference_population": 0.43453026,
"hom_count_reference_population": 154233,
"allele_count_reference_population": 701238,
"gnomad_exomes_af": 0.434175,
"gnomad_genomes_af": 0.437944,
"gnomad_exomes_ac": 634653,
"gnomad_genomes_ac": 66585,
"gnomad_exomes_homalt": 139525,
"gnomad_genomes_homalt": 14708,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": -0.6299999952316284,
"computational_prediction_selected": "Benign",
"computational_source_selected": "BayesDel_noAF",
"splice_score_selected": 0,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": null,
"revel_prediction": null,
"alphamissense_score": null,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.63,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 2.446,
"phylop100way_prediction": "Benign",
"spliceai_max_score": 0,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -21,
"acmg_classification": "Benign",
"acmg_criteria": "BP4_Strong,BP6_Very_Strong,BP7,BA1",
"acmg_by_gene": [
{
"score": -21,
"benign_score": 21,
"pathogenic_score": 0,
"criteria": [
"BP4_Strong",
"BP6_Very_Strong",
"BP7",
"BA1"
],
"verdict": "Benign",
"transcript": "ENST00000375708.4",
"gene_symbol": "ROR2",
"hgnc_id": 10257,
"effects": [
"synonymous_variant"
],
"inheritance_mode": "AR,AD",
"hgvs_c": "c.2088C>T",
"hgvs_p": "p.Tyr696Tyr"
}
],
"clinvar_disease": "Autosomal recessive Robinow syndrome,Brachydactyly type B1,not provided,not specified",
"clinvar_classification": "Benign",
"clinvar_review_status": "criteria provided, multiple submitters, no conflicts",
"clinvar_submissions_summary": "B:8",
"phenotype_combined": "not specified|Autosomal recessive Robinow syndrome|Brachydactyly type B1|not provided",
"pathogenicity_classification_combined": "Benign",
"custom_annotations": null
}
],
"message": null
}